draw_genotypes_admix {bnpsd} | R Documentation |
Given the Individual-specific Allele Frequency (IAF) matrix p_ind
for m
loci (rows) and n
individuals (columns), the genotype matrix X
(same dimensions as p_ind
) is drawn from the Binomial distribution equivalent to
X[ i, j ] <- rbinom( 1, 2, p_ind[ i, j ] )
,
except the function is more efficient.
If admix_proportions
is provided as the second argument (a matrix with n
individuals along rows and k
intermediate subpopulations along the columns), the first argument p_ind
is treated as the intermediate subpopulation allele frequency matrix (must be m
-by-k
) and the IAF matrix is equivalent to
p_ind %*% t( admix_proportions )
.
However, in this case the function computes the IAF matrix in parts only, never stored in full, greatly reducing memory usage.
If admix_proportions
is missing, then p_ind
is treated as the IAF matrix.
draw_genotypes_admix(p_ind, admix_proportions = NULL)
p_ind |
The |
admix_proportions |
The optional |
The m
-by-n
genotype matrix.
If admix_proportions
is missing, the row and column names of p_ind
are copied to this output.
If admix_proportions
is present, the row names of the output are the row names of p_ind
, while the column names of the output are the row names of admix_proportions
.
# dimensions # number of loci m_loci <- 10 # number of individuals n_ind <- 5 # number of intermediate subpops k_subpops <- 2 # define population structure # FST values for k = 2 subpops inbr_subpops <- c(0.1, 0.3) # non-trivial admixture proportions admix_proportions <- admix_prop_1d_linear(n_ind, k_subpops, sigma = 1) # draw allele frequencies # vector of ancestral allele frequencies p_anc <- draw_p_anc(m_loci) # matrix of intermediate subpop allele freqs p_subpops <- draw_p_subpops(p_anc, inbr_subpops) # matrix of individual-specific allele frequencies p_ind <- make_p_ind_admix(p_subpops, admix_proportions) # draw genotypes from intermediate subpops (one individual each) X_subpops <- draw_genotypes_admix(p_subpops) # and genotypes for admixed individuals X_ind <- draw_genotypes_admix(p_ind) # draw genotypes for admixed individuals without p_ind intermediate # (p_ind is computed internally in parts, never stored in full, # reducing memory use substantially) X_ind <- draw_genotypes_admix(p_subpops, admix_proportions)